Charlotta’s paper

Figures for Paper

DGE summary

  • differences between fetal and adult cells in general

Differential gene expression all adult v all fetal

DGE performed after removing outliers

Volcano plot

All adult v all fetal

GO

  • combine all changed genes between fetal and adult

GSEA using ProB

Laurenti Muschen using ProB only

Hallmark with ProB yeilds nothing

CMP

Using IL7R only fetal v adult

NO assotiation found with Laurenti gene lists.

Fetal v Adult IL7R only there is an enrichment in Hallmark genelists

G2M

E2F Targets

Epithelial to mesenchymal transition

KRAS signaling DN

hallmark myc targets

GSEA with Adult V fetal (in general)

## v7.0.1
## Downloading genesets to...
## /tmp/Rtmp8XWQ20
## - C1 -> 299 Gene Sets 
## - C2.CGP -> 3302 Gene Sets 
## - C2.CP -> 29 Gene Sets 
## - C2.CP.BIOCARTA -> 289 Gene Sets 
## - C2.CP.KEGG -> 186 Gene Sets 
## - C2.CP.PID -> 196 Gene Sets 
## - C2.CP.REACTOME -> 1499 Gene Sets 
## - C3.MIR -> 221 Gene Sets 
## - C3.TFT -> 610 Gene Sets 
## - C4.CGN -> 427 Gene Sets 
## - C4.CM -> 431 Gene Sets 
## - C5.BP -> 7350 Gene Sets 
## - C5.CC -> 1001 Gene Sets 
## - C5.MF -> 1645 Gene Sets 
## - C6 -> 189 Gene Sets 
## - C7 -> 4872 Gene Sets 
## - H -> 50 Gene Sets

KEGG

Reactome

UMAP/tSNE plot or PCA plot

  • only IL7R and proB from BM and all fetal stages
  • exclude CB, do with and without CS16 Laurenti Muschen using ProB only ### tSNE

PCA

UMAP

Take out CD34+CD38-CD45RA-

tSNE

PCA

UMAP

IL7R only

tSNE

PCA

DGE performed after HSCs taken out

Volcano plot

IL7R prog and proB from adult BM vs w12-13, w8-10 and CS samples - exclude CS16 for now

GO

  • combine all changed genes between fetal and adult

tryHyper

## v7.0.1
## Downloading genesets to...
## /tmp/Rtmp8XWQ20
## - C1 -> 299 Gene Sets 
## - C2.CGP -> 3302 Gene Sets 
## - C2.CP -> 29 Gene Sets 
## - C2.CP.BIOCARTA -> 289 Gene Sets 
## - C2.CP.KEGG -> 186 Gene Sets 
## - C2.CP.PID -> 196 Gene Sets 
## - C2.CP.REACTOME -> 1499 Gene Sets 
## - C3.MIR -> 221 Gene Sets 
## - C3.TFT -> 610 Gene Sets 
## - C4.CGN -> 427 Gene Sets 
## - C4.CM -> 431 Gene Sets 
## - C5.BP -> 7350 Gene Sets 
## - C5.CC -> 1001 Gene Sets 
## - C5.MF -> 1645 Gene Sets 
## - C6 -> 189 Gene Sets 
## - C7 -> 4872 Gene Sets 
## - H -> 50 Gene Sets

KEGG

Reactome

FPKM looking at previous data